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Jahanbani A, Amjadi J, Shooshtari H, Hasni R. On Degree Based Topological Properties of the Molecular Structure of Polycyclic Aromatic Hydrocarbons. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2159451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Akbar Jahanbani
- Department of Mathematics, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Jafar Amjadi
- Department of Mathematics, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Hajar Shooshtari
- Department of Mathematics, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Roslan Hasni
- Faculty of Ocean Engineering Technology and Informatics, University Malaysia Terengganu, Terengganu, Malaysia
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2
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Jahanbani A. Results about Molecular Structure of Chloroquine and Hydroxychloroquine for the Treatment Coronavirus. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2021.1934047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Akbar Jahanbani
- Department of Mathematics, Azarbaijan Shahid Madani University, Tabriz, Iran
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3
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Rosary MS. Topological Study of Line Graph of Remdesivir Compound Used in the Treatment of Corona Virus. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2021.1956552] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Maria Singaraj Rosary
- Department of Mathematics, Vel Tech High Tech Dr. Rangarajan Dr. Sakunthala Engineering College, Chennai, India
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4
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Ojbag J, Ilmakchi M. On Physical Analysis of Some Topological Indices for Hydroxychloroquine and Chloroquine. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2092874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- J. Ojbag
- Department of Mathematics, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - M. Ilmakchi
- Department of Mathematics, Azarbaijan Shahid Madani University, Tabriz, Iran
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5
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Xavier DA, Varghese ES, Baby A, Mathew D, K. A. Kaabar M. Distance based topological descriptors of Zinc Porphyrin Dendrimer. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Singh Y, Raza H, Sharma SK, Bhat VK. Computing Basis and Dimension of Chloroquine and Hydroxychloroquine by Using Chemical Graph Theory. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2086269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Yogesh Singh
- School of Electronics and Communication Engineering, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Hassan Raza
- School of Mathematical Sciences, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Sunny Kumar Sharma
- School of Mathematics, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Vijay Kumar Bhat
- School of Mathematics, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
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7
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Topological Study of 6.82 D Carbon Allotrope Structure. Symmetry (Basel) 2022. [DOI: 10.3390/sym14051037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Carbonallotropes are widely available and can be found in the atmosphere, the earth’s crust, and in living creatures in myriad forms. Allotropes are also used in several fields, including for medicinal and biological applications, due to their intriguing properties such as low resistance, high electron mobility, abnormal quantum hall effect, unconventional superconductivity in graphene, and so on. The theoretical analysis of carbon allotropes can hence be quite useful as it leads to a better understanding of the nature and behavior of these ubiquitous materials and also opens the door for even better applications. The objective of this research is to theoretically analyze the carbon allotrope by using four kinds of vertex degree based (VDB) topological indices (Tis), namely VDB multiplicative topological indices, VDB indices using M-Polynomial, VDB entropy measures, and irregularity indices. This analysis will extend the current body of knowledge available for this allotrope and help future researchers in the synthesis of new allotropes.
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8
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Wang J, Shi J, Jia N, Sun Q. Network pharmacology analysis reveals neuroprotection of Gynostemma pentaphyllum (Thunb.) Makino in Alzheimer' disease. BMC Complement Med Ther 2022; 22:57. [PMID: 35255879 PMCID: PMC8902721 DOI: 10.1186/s12906-022-03534-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/14/2022] [Indexed: 11/22/2022] Open
Abstract
Background Alzheimer’s disease (AD) is one of the most common neurodegenerative disorders in the world, but still lack of effective drug treatment. Gynostemma Pentaphyllum (Thunb.) Makino (GpM), a Chinese medicinal herb, plays important roles in anti-inflammation, anti-oxidative stress and anti-tumor, which has been reported to ameliorate cognitive impairment of AD. However, the neuroprotective mechanism of GpM remains unclear. This study aims to investigate the targets and possible signaling pathways of GpM in the treatment of AD. Methods Active compounds of GpM and their putative target proteins were selected from Traditional Chinese Medicine Systems Pharmacology (TCMSP) Database and Analysis Platform. AD-associated targets were identified from GeneCards, the Online Mendelian Inheritance in Man (OMIM) database and the Therapeutic Target Database (TTD). The intersecting targets of GpM and AD were identified and Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were carried out to analyze the mechanism of them. Compound-target-pathway (CTP) network and protein–protein interaction (PPI) network were constructed and analyzed to elucidate the correlation between compounds, proteins and pathways. Molecular docking was performed to further demonstrate the possibility of GpM for AD. Results A total of 13 active compounds of GpM, 168 putative target proteins of compounds and 722 AD-associated targets were identified. Eighteen intersecting targets of GpM and AD were found and the epidermal growth factor receptor (EGFR), interleukin-1 beta (IL-1β), interleukin-6 (IL-6), nitric oxide synthase in endothelial (NOS3) and serum paraoxonase/arylesterase 1 (PON1) were selected as the primary targets of GpM in the treatment of AD. The neuroprotective effect of GPM was related to a variety of pathways, including amoebiasis, HIF-1 signaling pathway, cytokine-cytokine receptor interaction and so on. Conclusions Our findings elucidate the active compounds, targets and pathways of GpM involved in effects of anti-AD. The novel mechanism of GpM against AD provides more treatment options for AD. Supplementary Information The online version contains supplementary material available at 10.1186/s12906-022-03534-z.
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Affiliation(s)
- Jiahao Wang
- Xi'an Jiaotong University Health Science Center , Xi'an, Shaanxi, 710061, People's Republic of China
| | - Jiamiao Shi
- Xi'an Jiaotong University Health Science Center , Xi'an, Shaanxi, 710061, People's Republic of China
| | - Ning Jia
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, No. 76, West Yanta Road, Xi'an, Shaanxi, 710061, People's Republic of China.
| | - Qinru Sun
- Institute of Forensic Medicine, Xi'an Jiaotong University Health Science Center, No. 76, West Yanta Road, Xi'an, Shaanxi, 710061, People's Republic of China.
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9
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PTML Modeling for Pancreatic Cancer Research: In Silico Design of Simultaneous Multi-Protein and Multi-Cell Inhibitors. Biomedicines 2022; 10:biomedicines10020491. [PMID: 35203699 PMCID: PMC8962338 DOI: 10.3390/biomedicines10020491] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 02/07/2023] Open
Abstract
Pancreatic cancer (PANC) is a dangerous type of cancer that is a major cause of mortality worldwide and exhibits a remarkably poor prognosis. To date, discovering anti-PANC agents remains a very complex and expensive process. Computational approaches can accelerate the search for anti-PANC agents. We report for the first time two models that combined perturbation theory with machine learning via a multilayer perceptron network (PTML-MLP) to perform the virtual design and prediction of molecules that can simultaneously inhibit multiple PANC cell lines and PANC-related proteins, such as caspase-1, tumor necrosis factor-alpha (TNF-alpha), and the insulin-like growth factor 1 receptor (IGF1R). Both PTML-MLP models exhibited accuracies higher than 78%. Using the interpretation from one of the PTML-MLP models as a guideline, we extracted different molecular fragments desirable for the inhibition of the PANC cell lines and the aforementioned PANC-related proteins and then assembled some of those fragments to form three new molecules. The two PTML-MLP models predicted the designed molecules as potentially versatile anti-PANC agents through inhibition of the three PANC-related proteins and multiple PANC cell lines. Conclusions: This work opens new horizons for the application of the PTML modeling methodology to anticancer research.
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10
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Amjadi J, Shooshtari H, Jahanbani A, Hasni R. Degree Based Weighted Entropy Indices of Polycyclic Aromatic Hydrocarbons. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2028868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jafar Amjadi
- Department of Mathematics, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Hajar Shooshtari
- Department of Mathematics, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Akbar Jahanbani
- Department of Mathematics, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Roslan Hasni
- Faculty of Ocean Engineering Technology and Informatics, University Malaysia Terengganu, Terengganu, Malaysia
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11
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Rosary MS. On Reverse Valency Based Topological Indices of Metal–Organic Framework. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2021.2021255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Maria Singaraj Rosary
- Department of Mathematics, Vel Tech High Tech Dr. Rangarajan Dr. Sakunthala Engineering College, Chennai, India
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12
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Speck-Planche A, Kleandrova VV, Scotti MT. In Silico Drug Repurposing for Anti-Inflammatory Therapy: Virtual Search for Dual Inhibitors of Caspase-1 and TNF-Alpha. Biomolecules 2021; 11:biom11121832. [PMID: 34944476 PMCID: PMC8699067 DOI: 10.3390/biom11121832] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/15/2021] [Accepted: 12/02/2021] [Indexed: 12/27/2022] Open
Abstract
Inflammation involves a complex biological response of the body tissues to damaging stimuli. When dysregulated, inflammation led by biomolecular mediators such as caspase-1 and tumor necrosis factor-alpha (TNF-alpha) can play a detrimental role in the progression of different medical conditions such as cancer, neurological disorders, autoimmune diseases, and cytokine storms caused by viral infections such as COVID-19. Computational approaches can accelerate the search for dual-target drugs able to simultaneously inhibit the aforementioned proteins, enabling the discovery of wide-spectrum anti-inflammatory agents. This work reports the first multicondition model based on quantitative structure–activity relationships and a multilayer perceptron neural network (mtc-QSAR-MLP) for the virtual screening of agency-regulated chemicals as versatile anti-inflammatory therapeutics. The mtc-QSAR-MLP model displayed accuracy higher than 88%, and was interpreted from a physicochemical and structural point of view. When using the mtc-QSAR-MLP model as a virtual screening tool, we could identify several agency-regulated chemicals as dual inhibitors of caspase-1 and TNF-alpha, and the experimental information later retrieved from the scientific literature converged with our computational results. This study supports the capabilities of our mtc-QSAR-MLP model in anti-inflammatory therapy with direct applications to current health issues such as the COVID-19 pandemic.
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Affiliation(s)
- Alejandro Speck-Planche
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, Brazil;
- Correspondence:
| | - Valeria V. Kleandrova
- Laboratory of Fundamental and Applied Research of Quality and Technology of Food Production, Moscow State University of Food Production, Volokolamskoe shosse 11, 125080 Moscow, Russia;
| | - Marcus T. Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, João Pessoa 58051-900, Brazil;
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13
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Artificial intelligence in drug design: algorithms, applications, challenges and ethics. FUTURE DRUG DISCOVERY 2021. [DOI: 10.4155/fdd-2020-0028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The discovery paradigm of drugs is rapidly growing due to advances in machine learning (ML) and artificial intelligence (AI). This review covers myriad faces of AI and ML in drug design. There is a plethora of AI algorithms, the most common of which are summarized in this review. In addition, AI is fraught with challenges that are highlighted along with plausible solutions to them. Examples are provided to illustrate the use of AI and ML in drug discovery and in predicting drug properties such as binding affinities and interactions, solubility, toxicology, blood–brain barrier permeability and chemical properties. The review also includes examples depicting the implementation of AI and ML in tackling intractable diseases such as COVID-19, cancer and Alzheimer’s disease. Ethical considerations and future perspectives of AI are also covered in this review.
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14
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On Ve-Degree-Based Irregularity Properties of the Crystallographic Structure of Molecules. J CHEM-NY 2021. [DOI: 10.1155/2021/9928543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Irregularity indices are usually used for quantitative characterization of the topological structure of nonregular graphs. In numerous applications and problems in material engineering and chemistry, it is useful to be aware that how irregular a molecular structure is? In this paper, we are interested in formulating closed forms of irregularity measures of some of the crystallographic structures of
and crystallographic structure of titanium difluoride of
. These theoretical conclusions provide practical guiding significance for pharmaceutical engineering and complex network and quantify the degree of folding of long organic molecules.
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15
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Wei J, Cancan M, Rehman AU, Siddiqui MK, Nasir M, Younas MT, Hanif MF. On Topological Indices of Remdesivir Compound Used in Treatment of Corona Virus (COVID 19). Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1887299] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jianxin Wei
- School of Mathematics and Statistics Science, Ludong University, Yantai, Shandong, 264025, China
| | - Murat Cancan
- Faculty of Education, Van Yuzuncu Yil University, Van, Turkey
| | - Atiq Ur Rehman
- Department of Mathematics, COMSATS University Islamabad, Lahore Campus, Pakistan
| | | | - Muhammad Nasir
- Department of Mathematics, COMSATS University Islamabad, Lahore Campus, Pakistan
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Sheikholeslami SM, Jahanbani A, Shao Z. On the molecular structure of Remdesivir for the treatment of Covid-19. Comput Methods Biomech Biomed Engin 2020; 24:995-1002. [PMID: 33356621 DOI: 10.1080/10255842.2020.1863380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
(SARS-CoV-2), was first identified in December 2019 as the cause of a respiratory illness designated coronavirus disease 2019, or Covid-19. Several therapeutic agents have been evaluated for the treatment of Covid-19, but none have yet been shown to be efficacious. Remdesivir (GS-5734), an inhibitor of the viral RNA-dependent, RNA polymerase with inhibitory activity against SARS-CoV and the Middle East respiratory syndrome (MERS-CoV), was identified early as a promising therapeutic candidate for Covid-19 because of its ability to inhibit SARS-CoV-2 in vitro. Besides, in nonhuman primate studies, remdesivir initiated 12 hours after inoculation with MERS-CoV9,10 reduced lung virus levels and lung damage. In the field of Medical Science, concerning the definition of the topological index on the molecular structure and corresponding medical, biological, chemical, pharmaceutical properties of drugs can be studied by the topological index calculation. In this paper, we compute some of the general temperature topological properties of remdesivir that the results in this paper may be useful in finding new drug and vaccine for the treatment and prevention of COVID-19.
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Affiliation(s)
- S M Sheikholeslami
- Department of Mathematics, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - A Jahanbani
- Department of Mathematics, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Z Shao
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
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17
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Julietraja K, Venugopal P. Computation of Degree-Based Topological Descriptors Using M-Polynomial for Coronoid Systems. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1804415] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- K. Julietraja
- Department of Mathematics, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, India
| | - P. Venugopal
- Department of Mathematics, Sri Sivasubramaniya Nadar College of Engineering, Kalavakkam, India
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18
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Jahanbani A, Shao Z, Sheikholeslami SM. Calculating degree based multiplicative topological indices of Hyaluronic Acid-Paclitaxel conjugates’ molecular structure in cancer treatment. J Biomol Struct Dyn 2020; 39:5304-5313. [DOI: 10.1080/07391102.2020.1800512] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Akbar Jahanbani
- Department of Mathematics, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Zehui Shao
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
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19
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Cancan M, Ediz S, Mutee-Ur-Rehman H, Afzal D. M-polynomial and topological indices Poly (EThyleneAmidoAmine) dendrimers. JOURNAL OF INFORMATION & OPTIMIZATION SCIENCES 2020. [DOI: 10.1080/02522667.2020.1745383] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Murat Cancan
- Faculty of Education, Van Yüzüncü Yıl University, Van 65090, Turkey
| | - Süleyman Ediz
- Department of Mathematics, Division of Science and Technology, University of Education, Lahore 54000, Pakistan
| | - Hafiz Mutee-Ur-Rehman
- Department of Mathematics and Statistics, The University of Lahore, Lahore 54000, Pakistan
| | - Deeba Afzal
- Department of Mathematics and Statistics, The University of Lahore, Lahore 54000, Pakistan
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20
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Shao Z, Jahanbani A, Sheikholeslami SM. Multiplicative Topological Indices of Molecular Structure in Anticancer Drugs. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1743329] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Zehui Shao
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
| | - Akbar Jahanbani
- Department of Mathematics, Azarbaijan Shahid Madani University, Tabriz, I.R. Iran
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21
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Zanni R, Garcia-Domenech R, Galvez-Llompart M, Galvez J. Alzheimer: A Decade of Drug Design. Why Molecular Topology can be an Extra Edge? Curr Neuropharmacol 2018; 16:849-864. [PMID: 29189164 PMCID: PMC6080094 DOI: 10.2174/1570159x15666171129102042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 09/26/2017] [Accepted: 10/10/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The last decade was characterized by a growing awareness about the severity of dementia in the field of age-related and no age-related diseases and about the importance to invest resources in the research of new, effective treatments. Among the dementias, Alzheimer's plays a substantial role because of its extremely high incidence and fatality. Several pharmacological strategies have been tried but still now, Alzheimer keeps being an untreatable disease. In literature, the number of QSAR related drug design attempts about new treatments for Alzheimer is huge, but only few results can be considered noteworthy. Providing a detailed analysis of the actual situation and reporting the most notable results in the field of drug design and discovery, the current review focuses on the potential of molecular topology as a reliable tool in finding new anti-Alzheimer lead compounds. METHODS Published works on QSAR applied to the search of anti-Alzheimer's drugs during the last 10 years has been tracked. 2D and 3D-QSAR, HQSAR, topological indexes, etc. have been analyzed, as well as different mechanisms of action, such as MAO, AchE, etc. An example of topological indexes' application to the search of potential anti-Alzheimer drugs is reported. RESULTS Results show that QSAR methods during the last decade represented an excellent approach to the search of new effective drugs against Alzheimer's. In particular, QSAR based on molecular topology allows the establishment of a direct structure-property link that results in the identification of new hits and leads. CONCLUSION Molecular topology is a powerful tool for the discovery of new anti-Alzheimer drugs covering simultaneously different mechanisms of action, what may help to find a definitive cure for the disease.
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Affiliation(s)
- Riccardo Zanni
- Molecular Topology and Drug Design Unit. Department of Physical Chemistry, University of Valencia, Valencia, Spain.,Department of Microbiology, University of Malaga, Malaga, Spain
| | - Ramon Garcia-Domenech
- Molecular Topology and Drug Design Unit. Department of Physical Chemistry, University of Valencia, Valencia, Spain
| | - Maria Galvez-Llompart
- Molecular Topology and Drug Design Unit. Department of Physical Chemistry, University of Valencia, Valencia, Spain.,Department of Microbiology, University of Malaga, Malaga, Spain
| | - Jorge Galvez
- Molecular Topology and Drug Design Unit. Department of Physical Chemistry, University of Valencia, Valencia, Spain
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22
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On Molecular Descriptors of Carbon Nanocones. Biomolecules 2018; 8:biom8030092. [PMID: 30205520 PMCID: PMC6164578 DOI: 10.3390/biom8030092] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 08/31/2018] [Accepted: 08/31/2018] [Indexed: 11/29/2022] Open
Abstract
Many degree-based topological indices can be obtained from the closed-off M-polynomial of a carbon nanocone. These topological indices are numerical parameters that are associated with a structure and, in combination, determine the properties of the carbon nanocone. In this paper, we compute the closed form of the M-polynomial of generalized carbon nanocone and recover many important degree-based topological indices. We use software Maple 2015 (Maplesoft, Waterloo, ON, Canada) to plot the surfaces and graphs associated with these nanocones, and relate the topological indices to the structure of these nanocones.
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23
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Chakraborty S, Rakshit J, Bandyopadhyay J, Basu S. Multi-functional neuroprotective activity of neohesperidin dihydrochalcone: a novel scaffold for Alzheimer's disease therapeutics identified via drug repurposing screening. NEW J CHEM 2018. [DOI: 10.1039/c8nj00853a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Multi-target screening identifies neohesperidin dihydrochalcone for Alzheimer's disease therapeutics, which exhibits strong BACE1 and amyloid aggregation inhibition along with antioxidant activity.
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Affiliation(s)
| | - Jyotirmoy Rakshit
- Department of Biotechnology
- Maulana Abul Kalam Azad University of Technology
- Kolkata 700064
- India
| | - Jaya Bandyopadhyay
- Department of Biotechnology
- Maulana Abul Kalam Azad University of Technology
- Kolkata 700064
- India
| | - Soumalee Basu
- Department of Microbiology
- University of Calcutta
- Kolkata – 700 019
- India
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24
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On Topological Indices of Certain Families of Nanostar Dendrimers. Molecules 2016; 21:molecules21070821. [PMID: 27347913 PMCID: PMC6273492 DOI: 10.3390/molecules21070821] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 05/11/2016] [Accepted: 06/07/2016] [Indexed: 11/16/2022] Open
Abstract
A topological index of graph G is a numerical parameter related to G which characterizes its molecular topology and is usually graph invariant. In the field of quantitative structure-activity (QSAR)/quantitative structure-activity structure-property (QSPR) research, theoretical properties of the chemical compounds and their molecular topological indices such as the Randić connectivity index, atom-bond connectivity (ABC) index and geometric-arithmetic (GA) index are used to predict the bioactivity of different chemical compounds. A dendrimer is an artificially manufactured or synthesized molecule built up from the branched units called monomers. In this paper, the fourth version of ABC index and the fifth version of GA index of certain families of nanostar dendrimers are investigated. We derive the analytical closed formulas for these families of nanostar dendrimers. The obtained results can be of use in molecular data mining, particularly in researching the uniqueness of tested (hyper-branched) molecular graphs.
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Pandey MK, DeGrado TR. Glycogen Synthase Kinase-3 (GSK-3)-Targeted Therapy and Imaging. Am J Cancer Res 2016; 6:571-93. [PMID: 26941849 PMCID: PMC4775866 DOI: 10.7150/thno.14334] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/27/2016] [Indexed: 12/11/2022] Open
Abstract
Glycogen synthase kinase-3 (GSK-3) is associated with various key biological processes, including glucose regulation, apoptosis, protein synthesis, cell signaling, cellular transport, gene transcription, proliferation, and intracellular communication. Accordingly, GSK-3 has been implicated in a wide variety of diseases and specifically targeted for both therapeutic and imaging applications by a large number of academic laboratories and pharmaceutical companies. Here, we review the structure, function, expression levels, and ligand-binding properties of GSK-3 and its connection to various diseases. A selected list of highly potent GSK-3 inhibitors, with IC50 <20 nM for adenosine triphosphate (ATP)-competitive inhibitors and IC50 <5 μM for non-ATP-competitive inhibitors, were analyzed for structure activity relationships. Furthermore, ubiquitous expression of GSK-3 and its possible impact on therapy and imaging are also highlighted. Finally, a rational perspective and possible route to selective and effective GSK-3 inhibitors is discussed.
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Ouyang L, He G, Huang W, Song X, Wu F, Xiang M. Combined structure-based pharmacophore and 3D-QSAR studies on phenylalanine series compounds as TPH1 inhibitors. Int J Mol Sci 2012; 13:5348-5363. [PMID: 22754301 PMCID: PMC3382768 DOI: 10.3390/ijms13055348] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 04/13/2012] [Accepted: 04/25/2012] [Indexed: 02/05/2023] Open
Abstract
Tryptophan hydroxylase-1 (TPH1) is a key enzyme in the synthesis of serotonin. As a neurotransmitter, serotonin plays important physiological roles both peripherally and centrally. In this study, a combination of ligand-based and structure-based methods is used to clarify the essential quantitative structure-activity relationship (QSAR) of known TPH1 inhibitors. A multicomplex-based pharmacophore (MCBP) guided method has been suggested to generate a comprehensive pharmacophore of TPH1 kinase based on three crystal structures of TPH1-inhibitor complex. This model has been successfully used to identify the bioactive conformation and align 32 structurally diverse substituted phenylalanine derivatives. The QSAR analyses have been performed on these TPH1 inhibitors based on the MCBP guided alignment. These results may provide important information for further design and virtual screening of novel TPH1 inhibitors.
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Affiliation(s)
- Liang Ouyang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; E-Mails: (L.O.); (X.S.); (F.W.); (M.X.)
| | - Gu He
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; E-Mails: (L.O.); (X.S.); (F.W.); (M.X.)
- Authors to whom correspondence should be addressed; E-Mails: (G.H.); (W.H.); Tel./Fax: +86-28-85503817 (G.H.); Tel./Fax: +86-28-61800231 (W.H.)
| | - Wei Huang
- State Key Laboratory Breeding Base of Systematic research, Development and Utilization of Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 610041, China
- Authors to whom correspondence should be addressed; E-Mails: (G.H.); (W.H.); Tel./Fax: +86-28-85503817 (G.H.); Tel./Fax: +86-28-61800231 (W.H.)
| | - Xiangrong Song
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; E-Mails: (L.O.); (X.S.); (F.W.); (M.X.)
| | - Fengbo Wu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; E-Mails: (L.O.); (X.S.); (F.W.); (M.X.)
| | - Mingli Xiang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; E-Mails: (L.O.); (X.S.); (F.W.); (M.X.)
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